Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Sequence”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

Crosslinking transcription factors to their recognition sequences with PtII complexes

We have prepared phosphorothioate-containing cyclic oligodeoxynucleotides that fold into 'dumbbells' containing CRE and TRE sequences, the binding sequences for the CREB and JUN proteins, respectively. Six phosphorothioate residues were introduced into each of the recognition sequences. K2PtCl4 crosslinks CRE to CREB and TRE to JUN. The extent of crosslinking is about eight times greater than that observed with standard oligodeoxynucleotides and amounts to 30-50% of the efficiency of non-covalent association as estimated by gel-shift assays. Crosslinking is reversed by incubation with NaCN. The crosslinking reaction is specific--a dumbbell oligonucleotide with six phosphorothioate groups introduced into the Sp1 recognition sequence could not be crosslinked efficiently to CREB or JUN proteins with K2PtCl4. The binding of TRE to CREB is not strong enough for effective detection by gel-shift assays, but the TRE-CREB complex is crosslinked efficiently by K2PtCl4 and can then readily be detected.

NASA Discipline Exobiology↗
NASA NTRS1992

How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.

Non-NASA Center↗
DOE OSTI2022

Controlling Rheology of Fluid Interfaces through Microblock Length of Sequence-Controlled Amphiphilic Copolymers

Previous studies have demonstrated that films of sequence-controlled amphiphilic copolymers display contact angles that depend on microblock size. This suggests that microblock length may provide a means of tuning surface and interfacial properties. In this work, the interfacial rheology of a series of sequence-controlled copolymers, prepared through the addition of bicyclo[4.2.0]oct-1(8)-ene-8-carboxamide (monomer A) and cyclohexene (monomer B) to generate sequences up to 24 monomeric units composed of (A m B n ) i microblocks, where m, n, and i range from 1 to 6. Interfacial rheometry is used to measure the mechanical properties of an air–water interface with these copolymers. As the microblock size increases, the interfacial storage modulus, G', increases, which may be due to an increase in the size of interfacial hydrophobic domains. Small-angle X-ray scattering shows that the copolymers have a similar conformation in solution, suggesting that any variations in the mechanics of the interface are due to assembly at the interface, and not on solution association or bulk rheological properties. This is the first study demonstrating that microblock size can be used to control interfacial rheology of amphiphilic copolymers. Here, the results provide a new strategy for controlling the dynamics of fluid interfaces through precision sequence-controlled polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Evaluating the mutagenicity of N-nitrosodimethylamine in 2D and 3D HepaRG cell cultures using error-corrected next generation sequencing

Human liver-derived metabolically competent HepaRG cells have been successfully employed in both two-dimensional (2D) and 3D spheroid formats for performing the comet assay and micronucleus (MN) assay. In the present study, we have investigated expanding the genotoxicity endpoints evaluated in HepaRG cells by detecting mutagenesis using two error-corrected next generation sequencing (ecNGS) technologies, Duplex Sequencing (DS) and High-Fidelity (HiFi) Sequencing. Both HepaRG 2D cells and 3D spheroids were exposed for 72 h to N-nitrosodimethylamine (NDMA), followed by an additional incubation for the fixation of induced mutations. NDMA-induced DNA damage, chromosomal damage, and mutagenesis were determined using the comet assay, MN assay, and ecNGS, respectively. The 72-h treatment with NDMA resulted in concentration-dependent increases in cytotoxicity, DNA damage, MN formation, and mutation frequency in both 2D and 3D cultures, with greater responses observed in the 3D spheroids compared to 2D cells. The mutational spectrum analysis showed that NDMA induced predominantly A:T → G:C transitions, along with a lower frequency of G:C → A:T transitions, and exhibited a different trinucleotide signature relative to the negative control. These results demonstrate that the HepaRG 2D cells and 3D spheroid models can be used for mutagenesis assessment using both DS and HiFi Sequencing, with the caveat that severe cytotoxic concentrations should be avoided when conducting DS. With further validation, the HepaRG 2D/3D system may become a powerful human-based metabolically competent platform for genotoxicity testing.

3D spheroids↗
DOE OSTI2022

Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04

Algae are a broad class of photosynthetic eukaryotes that are phylogenetically and physiologically diverse. Most of the phylogenetic diversity has been inferred from 18S rDNA sequencing since there are only a few complete genomes available in public databases. Here we use ultra-long-read Nanopore sequencing to determine a gapless, telomere-to-telomere complete genome sequence of Chlorella sp. SLA-04, previously described as Chlorella sorokiniana SLA-04. Chlorella sp. SLA-04 is a green alga that grows to high cell density in a wide variety of environments - high and neutral pH, high and low alkalinity, and high and low salinity. SLA-04's ability to grow in high pH and high alkalinity media without external CO 2 supply is favorable for large-scale algal biomass production. Phylogenetic analysis performed using ribosomal DNA and conserved protein sequences consistently reveal that Chlorella sp. SLA-04 forms a distinct lineage from other strains of Chlorella sorokiniana. We complement traditional genome annotation methods with high throughput structural predictions and demonstrate that this approach expands functional prediction of the SLA-04 proteome. Genomic analysis of the SLA-04 genome identifies the genes capable of utilizing TCA cycle intermediates to replenish cytosolic acetyl-CoA pools for lipid production. We also identify a complete metabolic pathway for sphingolipid anabolism that may allow SLA-04 to readily adapt to changing environmental conditions and facilitate robust cultivation in mass production systems. Altogether, this work clarifies the phylogeny of Chlorella sp. SLA-04 within Trebouxiophyceae and demonstrates how structural predictions can be used to improve annotation beyond sequencebased methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Potential for constraining sequence stratigraphy and cycle stratigraphy with U-Pb dating of carbonates

Studies of sequence stratigraphy and cycle stratigraphy in carbonate formations increasingly improve our understanding of depositional systems and basinal to global correlations. However, there is still a scarcity of dated sequences to determine the time length of sequences and cycles. Furthermore, the durations of sequences and cycles provide tests of the processes that produce them. Poor age resolution mostly stems from the lack of recognizable volcanic ash deposits in many sections. Through continuing advances in analytical techniques and approaches to sampling, the current state of Usingle bondPb dating of carbonate sedimentary rocks provides opportunities to fill in age gaps. The approach should build on well-constrained 3-dimensional stratigraphic architectures and diagenetic stratigraphies.

58 GEOSCIENCES↗
DOE OSTI2020

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

Summary: We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses. - Highlights: • The complete genome of alfalfa dwarf virus is obtained. • An integrated localization and interaction map for ADV is determined. • ADV has a genome sequence similarity and evolutionary links with cytorhabdoviruses. • ADV protein localization and interaction data show an association with the nucleus. • ADV combines properties of both cytoplasmic and nuclear plant rhabdoviruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

RADIO AND MID-INFRARED PROPERTIES OF COMPACT STARBURSTS: DISTANCING THEMSELVES FROM THE MAIN SEQUENCE

We investigate the relationship between 8.44 GHz brightness temperatures and 1.4 to 8.44 GHz radio spectral indices with 6.2 {mu}m polycyclic aromatic hydrocarbon (PAH) emission and 9.7 {mu}m silicate absorption features for a sample of 36 local luminous and ultraluminous infrared galaxies. We find that galaxies having small 6.2 {mu}m PAH equivalent widths (EQWs), which signal the presence of weak PAH emission and/or an excess of very hot dust, also have flat spectral indices. The three active galactic nuclei (AGN) identified through their excessively large 8.44 GHz brightness temperatures are also identified as AGN via their small 6.2 {mu}m PAH EQWs. We also find that the flattening of the radio spectrum increases with increasing silicate optical depth, 8.44 GHz brightness temperature, and decreasing size of the radio source even after removing potential AGN, supporting the idea that compact starbursts show spectral flattening as the result of increased free-free absorption. These correlations additionally suggest that the dust obscuration in these galaxies must largely be coming from the vicinity of the compact starburst itself, and is not distributed throughout the (foreground) disk of the galaxy. Finally, we investigate the location of these infrared-bright systems relative to the main sequence (star formation rate versus stellar mass) of star-forming galaxies in the local universe. We find that the radio spectral indices of galaxies flatten with increasing distance above the main sequence, or in other words, with increasing specific star formation rate. This indicates that galaxies located above the main sequence, having high specific star formation rates, are typically compact starbursts hosting deeply embedded star formation that becomes more optically thick in the radio and infrared with increased distance above the main sequence.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Possible evidence for metal accretion onto the surfaces of metal-poor main-sequence stars

The entire evolution of the Milky Way, including its mass-assembly and star-formation history, is imprinted onto the chemo-dynamical distribution function of its member stars, f(x, v, [X/H]), in the multi-dimensional phase space spanned by position, velocity, and elemental abundance ratios. In particular, the chemo-dynamical distribution functions for low-mass stars (e.g., G- or K-type dwarfs) are precious tracers of the earliest stages of the Milky Way's formation, since their main-sequence lifetimes approach or exceed the age of the universe. A basic tenet of essentially all previous analyses is that the stellar metallicity, usually parameterized as [Fe/H], is conserved over time for main-sequence stars (at least those that have not been polluted due to mass transfer from binary companions). If this holds true, any correlations between metallicity and kinematics for long-lived main-sequence stars of different masses, effective temperatures, or spectral types must strictly be the same, since they reflect the same mass-assembly and star-formation histories. By analyzing a sample of nearby metal-poor halo and thick-disk stars on the main sequence, taken from Data Release 8 of the Sloan Digital Sky Survey, we find that the median metallicity of G-type dwarfs is systematically higher (by about 0.2 dex) than that of K-type dwarfs having the same median rotational velocity about the Galactic center. If it can be confirmed, this finding may invalidate the long-accepted assumption that the atmospheric metallicities of long-lived stars are conserved over time.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

MAIN-SEQUENCE STARS MASQUERADING AS YOUNG STELLAR OBJECTS IN THE CENTRAL MOLECULAR ZONE

In contrast to most other galaxies, star formation rates in the Milky Way can be estimated directly from young stellar objects (YSOs). In the central molecular zone the star formation rate calculated from the number of YSOs with 24 μm emission is up to an order of magnitude higher than the value estimated from methods based on diffuse emission (such as free-free emission). Whether this effect is real or whether it indicates problems with either or both star formation rate measures is not currently known. In this paper, we investigate whether estimates based on YSOs could be heavily contaminated by more evolved objects such as main-sequence stars. We present radiative transfer models of YSOs and of main-sequence stars in a constant ambient medium which show that the main-sequence objects can indeed mimic YSOs at 24 μm. However, we show that in some cases the main-sequence models can be marginally resolved at 24 μm, whereas the YSO models are always unresolved. Based on the fraction of resolved MIPS 24 μm sources in the sample of YSOs previously used to compute the star formation rate, we estimate the fraction of misclassified ''YSOs'' to be at least 63%, which suggests that the star formation rate previously determined from YSOs is likely to be at least a factor of three too high.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

ADIABATIC MASS LOSS IN BINARY STARS. II. FROM ZERO-AGE MAIN SEQUENCE TO THE BASE OF THE GIANT BRANCH

In the limit of extremely rapid mass transfer, the response of a donor star in an interacting binary becomes asymptotically one of adiabatic expansion. We survey here adiabatic mass loss from Population I stars (Z = 0.02) of mass 0.10 M{sub ⊙}–100 M{sub ⊙} from the zero-age main sequence to the base of the giant branch, or to central hydrogen exhaustion for lower main sequence stars. The logarithmic derivatives of radius with respect to mass along adiabatic mass-loss sequences translate into critical mass ratios for runaway (dynamical timescale) mass transfer, evaluated here under the assumption of conservative mass transfer. For intermediate- and high-mass stars, dynamical mass transfer is preceded by an extended phase of thermal timescale mass transfer as the star is stripped of most of its envelope mass. The critical mass ratio q{sub ad} (throughout this paper, we follow the convention of defining the binary mass ratio as q ≡ M{sub donor}/M{sub accretor}) above which this delayed dynamical instability occurs increases with advancing evolutionary age of the donor star, by ever-increasing factors for more massive donors. Most intermediate- or high-mass binaries with nondegenerate accretors probably evolve into contact before manifesting this instability. As they approach the base of the giant branch, however, and begin developing a convective envelope, q{sub ad} plummets dramatically among intermediate-mass stars, to values of order unity, and a prompt dynamical instability occurs. Among low-mass stars, the prompt instability prevails throughout main sequence evolution, with q{sub ad} declining with decreasing mass, and asymptotically approaching q{sub ad} = 2/3, appropriate to a classical isentropic n = 3/2 polytrope. Our calculated q{sub ad} values agree well with the behavior of time-dependent models by Chen and Han of intermediate-mass stars initiating mass transfer in the Hertzsprung gap. Application of our results to cataclysmic variables, as systems that must be stable against rapid mass transfer, nicely circumscribes the range in q{sub ad} as a function of the orbital period in which they are found. These results are intended to advance the verisimilitude of population synthesis models of close binary evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys

The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable region of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Altogether, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Influence of Control and Limiter Schemes on Sequence-Domain Fault Models of Grid-Forming Inverter-Interfaced Distributed Generators

Unlike synchronous generators, the fault response of grid-forming (GFM) inverter-interfaced distributed generators (IIDGs) is notably governed by the selection of control and current limiting strategies rather than inherent physical traits. While recent research has focused on the sequence domain fault model of GFM IIDGs, a research gap exists in elucidating the influence of control and current limiting schemes on this model's characteristics. This article aims to fill this void by examining how different control and current limiting schemes influence the positive and negative sequence impedances in the phasor-domain fault model of GFM IIDGs. This investigation encompasses droop-based, virtual synchronous machine-based, and virtual oscillator-based reference generation controls alongside rotating and stationary reference-frame-based voltage controls. Furthermore, saturation-based, latching-based, circular and virtual impedance-based current limiting schemes are analyzed. To achieve this goal, a thorough numerical simulation study is conducted. Findings indicate that outer reference generation controls exhibit minimal impact. Conversely, the choice of voltage control and various current limiting schemes emerge as the predominant factors shaping the sequence models of GFM IIDGs. These analyses and results are instrumental in devising reliable protection strategies within inverter-based grids, as a comprehensive understanding of electrical elements in the sequence domain is imperative for effective protective measures.

current limiters↗
DOE OSTI2022

Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing

Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/μL of sample for SWGA and >129 genomic copies/μL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Newborn Screening Quality Assurance Program for CFTR Mutation Detection and Gene Sequencing to Identify Cystic Fibrosis

All newborn screening laboratories in the United States and many worldwide screen for cystic fibrosis. Most laboratories use a second-tier genotyping assay to identify a panel of mutations in the CF transmembrane regulator (CFTR) gene. Centers for Disease Control and Prevention’s Newborn Screening Quality Assurance Program houses a dried blood spot repository of samples containing CFTR mutations to assist newborn screening laboratories and ensure high-quality mutation detection in a high-throughput environment. Recently, CFTR mutation detection has increased in complexity with expanded genotyping panels and gene sequencing. To accommodate the growing quality assurance needs, the repository samples were characterized with several multiplex genotyping methods, Sanger sequencing, and 3 next-generation sequencing assays using a high-throughput, low-concentration DNA extraction method. The samples performed well in all of the assays, providing newborn screening laboratories with a resource for complex CFTR mutation detection and next-generation sequencing as they transition to new methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps

Abstract The information about the domain architecture of proteins is useful for studying protein structure and function. However, accurate prediction of protein domain boundaries (i.e., sequence regions separating two domains) from sequence remains a significant challenge. In this work, we develop a deep learning method based on multi-head U-Nets (called DistDom) to predict protein domain boundaries utilizing 1D sequence features and predicted 2D inter-residue distance map as input. The 1D features contain the evolutionary and physicochemical information of protein sequences, whereas the 2D distance map includes the structural information of proteins that was rarely used in domain boundary prediction before. The 1D and 2D features are processed by the 1D and 2D U-Nets respectively to generate hidden features. The hidden features are then used by the multi-head attention to predict the probability of each residue of a protein being in a domain boundary, leveraging both local and global information in the features. The residue-level domain boundary predictions can be used to classify proteins as single-domain or multi-domain proteins. It classifies the CASP14 single-domain and multi-domain targets at the accuracy of 75.9%, 13.28% more accurate than the state-of-the-art method. Tested on the CASP14 multi-domain protein targets with expert annotated domain boundaries, the average per-target F1 measure score of the domain boundary prediction by DistDom is 0.263, 29.56% higher than the state-of-the-art method.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models

Abstract Background Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). Here, we describe an FPGA hardware accelerator, called HAVAC, that targets a key bottleneck step (SSV) in the analysis pipeline of the popular pHMM alignment tool, HMMER. Results The HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a $$\sim$$ ∼ $3000 Xilinx Alveo U50 FPGA accelerator card, $$\sim$$ ∼ 227× faster than the optimized SSV implementation in nhmmer . Accounting for PCI-e data transfer data processing, HAVAC is 65× faster than nhmmer’s SSV with one thread and 35× faster than nhmmer with four threads, and uses $$\sim$$ ∼ 31% the energy of a traditional high end Intel CPU. Conclusions HAVAC demonstrates the potential offered by FPGA hardware accelerators to produce dramatic speed gains in sequence annotation and related bioinformatics applications. Because these computations are performed on a co-processor, the host CPU remains free to simultaneously compute other aspects of the analysis pipeline.

59 BASIC BIOLOGICAL SCIENCES↗